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- PDB-4ybq: Rat GLUT5 with Fv in the outward-open form -

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Basic information

Entry
Database: PDB / ID: 4ybq
TitleRat GLUT5 with Fv in the outward-open form
Components
  • Solute carrier family 2, facilitated glucose transporter member 5
  • antibody Fv fragment heavy chain
  • antibody Fv fragment light chain
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / SUGAR TRANSPORTER / MAJOR FACILITATOR SUPERFAMILY / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Intestinal hexose absorption / regulation of systemic arterial blood pressure mediated by a chemical signal / fructose transmembrane transporter activity / fructose import across plasma membrane / fructose transmembrane transport / fructose binding / D-glucose transmembrane transporter activity / metanephric proximal tubule development / D-glucose transmembrane transport / cellular response to fructose stimulus ...Intestinal hexose absorption / regulation of systemic arterial blood pressure mediated by a chemical signal / fructose transmembrane transporter activity / fructose import across plasma membrane / fructose transmembrane transport / fructose binding / D-glucose transmembrane transporter activity / metanephric proximal tubule development / D-glucose transmembrane transport / cellular response to fructose stimulus / response to fructose / Neutrophil degranulation / sarcolemma / apical plasma membrane / plasma membrane
Similarity search - Function
Fructose transporter, type 5 (GLUT5) / Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / MFS general substrate transporter like domains / Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Growth Hormone; Chain: A; ...Fructose transporter, type 5 (GLUT5) / Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / MFS general substrate transporter like domains / Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Solute carrier family 2, facilitated glucose transporter member 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsNomura, N. / Shimamura, T. / Iwata, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Nature / Year: 2015
Title: Structure and mechanism of the mammalian fructose transporter GLUT5
Authors: Nomura, N. / Verdon, G. / Kang, H.J. / Shimamura, T. / Nomura, Y. / Sonoda, Y. / Hussien, S.A. / Qureshi, A.A. / Coincon, M. / Sato, Y. / Abe, H. / Nakada-Nakura, Y. / Hino, T. / Arakawa, T. ...Authors: Nomura, N. / Verdon, G. / Kang, H.J. / Shimamura, T. / Nomura, Y. / Sonoda, Y. / Hussien, S.A. / Qureshi, A.A. / Coincon, M. / Sato, Y. / Abe, H. / Nakada-Nakura, Y. / Hino, T. / Arakawa, T. / Kusano-Arai, O. / Iwanari, H. / Murata, T. / Kobayashi, T. / Hamakubo, T. / Kasahara, M. / Iwata, S. / Drew, D.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Solute carrier family 2, facilitated glucose transporter member 5
B: Solute carrier family 2, facilitated glucose transporter member 5
C: antibody Fv fragment light chain
D: antibody Fv fragment heavy chain
E: antibody Fv fragment light chain
F: antibody Fv fragment heavy chain


Theoretical massNumber of molelcules
Total (without water)169,4726
Polymers169,4726
Non-polymers00
Water00
1
A: Solute carrier family 2, facilitated glucose transporter member 5
E: antibody Fv fragment light chain
F: antibody Fv fragment heavy chain


Theoretical massNumber of molelcules
Total (without water)84,7363
Polymers84,7363
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Solute carrier family 2, facilitated glucose transporter member 5
C: antibody Fv fragment light chain
D: antibody Fv fragment heavy chain


Theoretical massNumber of molelcules
Total (without water)84,7363
Polymers84,7363
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.773, 151.541, 106.396
Angle α, β, γ (deg.)90.00, 97.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Solute carrier family 2, facilitated glucose transporter member 5 / Fructose transporter / Glucose transporter type 5 / small intestine / GLUT-5


Mass: 56425.801 Da / Num. of mol.: 2 / Mutation: N50Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc2a5, Glut5 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P43427
#2: Antibody antibody Fv fragment light chain


Mass: 13446.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Brevibacillus choshinensis (bacteria)
#3: Antibody antibody Fv fragment heavy chain


Mass: 14863.454 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Brevibacillus choshinensis (bacteria)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 33-35% PEG400, 0.12 M CaCl2, 0.1 M Tris-HCl pH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.27→50 Å / Num. obs: 38017 / % possible obs: 99.9 % / Redundancy: 13 % / Net I/σ(I): 1.22

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O7Q

3o7q


Resolution: 3.27→36.491 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2881 1842 4.94 %Random selection
Rwork0.2419 ---
obs0.2442 37289 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.27→36.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10657 0 0 0 10657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410901
X-RAY DIFFRACTIONf_angle_d0.97214793
X-RAY DIFFRACTIONf_dihedral_angle_d11.8993862
X-RAY DIFFRACTIONf_chiral_restr0.0361716
X-RAY DIFFRACTIONf_plane_restr0.0051840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.27-3.35840.38881440.34412723X-RAY DIFFRACTION100
3.3584-3.45710.38261450.31472692X-RAY DIFFRACTION100
3.4571-3.56860.34391380.29832711X-RAY DIFFRACTION100
3.5686-3.69610.32671490.27582720X-RAY DIFFRACTION100
3.6961-3.84390.3071570.24962721X-RAY DIFFRACTION100
3.8439-4.01860.2811480.22822709X-RAY DIFFRACTION100
4.0186-4.23020.24941310.21472734X-RAY DIFFRACTION100
4.2302-4.49480.2441470.19022719X-RAY DIFFRACTION100
4.4948-4.84110.23231400.19552725X-RAY DIFFRACTION100
4.8411-5.3270.27931420.22732723X-RAY DIFFRACTION100
5.327-6.09470.32341320.26732741X-RAY DIFFRACTION100
6.0947-7.66690.32671320.27592781X-RAY DIFFRACTION100
7.6669-36.49330.27441370.23552748X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9343-0.3183-0.28162.08460.84453.24440.11610.2265-0.49450.1976-0.16620.23050.5457-0.6965-0.02520.4314-0.1071-0.02550.8537-0.02950.70528.0605-19.908126.3221
24.2263-0.2261.37212.1193-0.4725.3260.3277-0.4261-0.04510.1361-0.0349-0.39050.45730.1225-0.13080.3735-0.05870.01810.7396-0.02480.7415117.7244-2.7865167.1603
32.6862-0.1299-0.11264.6813-1.70344.8220.24050.34350.2002-0.2103-0.21391.7358-0.19030.1273-0.06460.55920.0098-0.05420.9948-0.25121.393576.283917.6763148.7588
44.3167-0.83134.09227.5089-14.2423-0.92870.11191.4743-0.76760.07620.248-0.4639-1.11220.73930.7237-0.0986-0.04920.91740.1061.052990.011231.6695141.278
59.27510.79220.58955.77120.00610.16390.2454-1.2734-0.42120.2449-0.6911-0.1944-0.05981.76890.17020.6896-0.2224-0.00822.02860.29891.160669.25737.0419124.0377
65.17544.0131-1.61947.33960.05314.38581.06331.3863.7984-0.73560.38371.5656-1.239-0.8932-0.56610.82940.07660.39050.88030.16771.878955.439922.043119.1056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 480)
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 480)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 115)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 120)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 115)
6X-RAY DIFFRACTION6(chain 'F' and resid 2 through 120)

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